Introduction To R | Session 1

First things first

Get going by downloading and installing R and RStudio (in that order).

Learning objectives

Session 1

Introduction to R and RStudio
Basic data types
Functions
Arithmetic and logical operators
Vectors, data frames, and factors
Indexing
Reading data
Plotting with base R

RStudio

RStudio has a four panel layout: documents, console, environment, and stuff (plots, help, files, …)

Set the working directory (Session > Set Working Directory) to the working_area folder
Open a new document … File > New File >:
- R Notebook: allows you to interleave R code, comments, and images. An HTML is automatically produced that records the last outputs when the document is saved
- R Markdown: the same, but will an HTML is only produced when asked, and all code is re-run (knit) before it’s produced
Commands run in the documents pane and in the console will behave identically. Run a line of code with ⌘+Enter (Mac) or CTRL+Enter (Windows), or by typing it into the console directly.
Run individual or highlighted lines of code with ⌘+Shift+Enter (Mac) or CTRL+Shift+Enter (Windows)
Insert a code block at the position of the cursor with ⌘+⌥+I (Mac) or CTRL+Alt+I (Windows)
Press the ⏵ (run) button to run a code block
Press ⌘+S (Mac) or CTRL+S (Windows) to save

Assignment

Let’s try some basic calculations. R knows all the usual arithmetic operators: +, -, /, *, and ^. By default, results are printed to the screen.

1 + 1

## [1] 2

To store an answer, we must assign it with either the <- or = operator.

a <- 10 / 2  # is the same ...
a = 10 / 2   # ... as this

Here, an object (or variable), a, is created to store the calculation’s result. We can query what a stores.

## [1] 5

Assignment works from right to left. Here, we can say that b becomes equal to the result of sqrt(25).

b = sqrt(25)
b

## [1] 5

Stored objects appear in RStudio’s environment panel. As in algebra, they can be used in calculations.

a * b

## [1] 25

Assigning to an existing object will overwrite its previous value.

a = a * b
a

## [1] 25

Comments

Comments in your code allow you to keep track of your ideas and to document your work. In R, on each line, everything after a # symbol is considered a comment and will not be run.

# This whole line is a comment

a = a * b  # This is a comment as well!

We can highjack this system to ‘comment out’ code sections if we don’t want them to run.

# The following calculation will not run:
# a = a * b

For the current or highlighted lines, the ⌘+Shift+C (Mac) or CTRL+Shift+C (Windows) will comment and un-comment lines for you in RStudio.

Object naming

As in all programming languages, in R, there are rules about what names an object can be given.

Object names cannot start with a number …

1var = 1  # will fail

… contain special characters (e.g. a minus sign) …

my-variable = 1  # will also fail

… or contain spaces.

my variable = 1  # will also also fail

Object names can only contain, numbers, characters, underscores, and points.

Names should be short and meaningful so that you can type them easily and know what they store.

tcga_data = ...  # a nice, short, meaningful name

the_data_we_got_from_that_2019_paper = ...  # not a good name!

t = ...  # tulip? turtle? time?

As spaces aren’t allowed, there are are two preferred options instead.

this_is_called_snake_case = "hello"

thisIsCalledCamelCase = "world"

Functions

sqrt() was an example of a function. A function runs a pre-determined calculation or procedure, generally (but not always) returning an answer.

one_to_ten = seq(1, 10)
one_to_ten

##  [1]  1  2  3  4  5  6  7  8  9 10

min(one_to_ten)

## [1] 1

max(one_to_ten)

## [1] 10

R is extremely well documented. To find out what a function does or how to use it, use the ? operator.

?mean

Arithmetic Mean

Description
  Generic function for the (trimmed) arithmetic mean.

Usage
  mean(x, ...)

## Default S3 method:
  mean(x, trim = 0, na.rm = FALSE, ...)

...

We can also ask R to give an example of the function in use … though some are a bit complicated!

example("mean")

The full function signature for mean() is mean(x, trim = 0, na.rm = FALSE, ...).

Breaking it down:

the function name is mean
inputs to the function - its arguments - are provided within the brackets
required arguments do not have a preset value (e.g. x). They are generally positional so that, provided you pass them in the correct order, you don’t have to specify their names.

mean(one_to_ten)  # is the same as ...
mean(x=one_to_tex)  # ... this. The names of positional arguments are implicit

optional arguments have a preset value (e.g. trim = 0) and, if they’re not specified, the preset will be used. For clarity, when we do specify optional arguments, it’s good practice to use their names.

mean(one_to_ten, trim=0.1)

Practical

Ask R what these functions do:

mad
ceiling
floor
toupper
range

Basic data types

There are three basic data types that we use in R day-to-day:

Numeric values store a number (with the subclasses integer and double)
Character values (aka a string of characters) wrapped in quotation marks store text
Logical values (aka a boolean) store a TRUE/FALSE result

The type of an object can be determined using the class() function.

class(1)

## [1] "numeric"

class("this is a string")

## [1] "character"

Vectors

Basic data types can be grouped into collections of elements. A vector is one of the most fundamental, storing elements of the same type.

The c() function combines the given elements, flattening any other vectors along the way.

c(1, 2, 3)

## [1] 1 2 3

c("one", "two", "three", c("four", "five"))

## [1] "one"   "two"   "three" "four"  "five"

c(TRUE, FALSE, T, F)

## [1]  TRUE FALSE  TRUE FALSE

There are a number of handy functions for creating vectors.

The seq() function (or the : operator) will create a sequence of numbers

seq(11, 20)

##  [1] 11 12 13 14 15 16 17 18 19 20

11:20

##  [1] 11 12 13 14 15 16 17 18 19 20

The rep() function will repeat a given object a specified number of times

a = rep(11:15, 3)
a

##  [1] 11 12 13 14 15 11 12 13 14 15 11 12 13 14 15

Practical

Let’s work out what these will do when making a vector:

seq(1, 10, 2)
10:1
c(1:10, 10:1)

R is vectorised

Many of the core R functions are vectorised - i.e. functions are written to operate on all elements of a vector simultaneously.

Vector operations avoid the need to loop through and act on each element individually, making writing code more concise and less error prone. They’re also much faster!

a ^ 2

##  [1] 121 144 169 196 225 121 144 169 196 225 121 144 169 196 225

log(a)

##  [1] 2.397895 2.484907 2.564949 2.639057 2.708050 2.397895 2.484907 2.564949
##  [9] 2.639057 2.708050 2.397895 2.484907 2.564949 2.639057 2.708050

Indexing vectors

Specific elements can be extracted from vectors by their position (or index) using square brackets ([ ]).

a[5]

## [1] 15

a[1:3]

## [1] 11 12 13

Conversely, specific elements can be excluded by using a minus sign.

a[-c(1, 3, 5)]

##  [1] 12 14 11 12 13 14 15 11 12 13 14 15

The order of index values matters; [c(1, 2)] is different to [c(2, 1)]). The order of the supplied index values can be used to arrange data, therefore.

a[15:1]

##  [1] 15 14 13 12 11 15 14 13 12 11 15 14 13 12 11

order() sorts a vector and returns the index values in the order that achieve this representation.

order(a)

##  [1]  1  6 11  2  7 12  3  8 13  4  9 14  5 10 15

a[order(a)]

##  [1] 11 11 11 12 12 12 13 13 13 14 14 14 15 15 15

Name-based indexing of vectors is also possible.

Names can be assigned to an existing vector by using the names() function.

a = c(1, 2, 3)
names(a) = c("first", "second", "third")
a

##  first second  third 
##      1      2      3

Alternatively, names can be supplied when the vector is first created.

a = c(first=1, second=2, third=3)
a

##  first second  third 
##      1      2      3

Named vectors can be indexed using square brackets ([ ]) (to retain the names) or with double square brackets ([[ ]]) (to discard them).

a["second"]

## second 
##      2

a[["second"]]

## [1] 2

Indexing does not work beyond the bounds of a vector, however - you can’t index beyond its length

length(a)

## [1] 3

a[4]

## <NA> 
##   NA

Here, R uses the NA (not available) logical constant to signify that a value is missing.

Similarly, you can’t index a named vector with a name that it does not contain.

names(a)

## [1] "first"  "second" "third"

a["fourth"]

## <NA> 
##   NA

Again, R uses the NA (not available) logical constant to signify that a value is missing.

Practical

You have inherited 4 penguins from an estranged aunt!

Make a vector that records their ages in months: 15, 53, 97, and 64.
Have you chosen a good name?
Add the information that their names are Basil, Tim, Lisa, and Snapper.
What are their ages in complete years?
What is the median age of your penguins?

Index-based replacement

Specific elements within vectors can be replaced by referencing their index in an assignment operation. This works identically for position-based and name-based indexing.

a[1:2] = 0
a

##  first second  third 
##      0      0      3

a[c("first", "second")] = c(1, 2)
a

##  first second  third 
##      1      2      3

Logical operations

Two objects can be compared to one another using logical operations:

x == y … is equal to
x != y … is not equal to
x > y … is greater than (>= or equal to)
x < y … is less than (<= or equal to)

These return a logical TRUE/FALSE answer.

1 > 2

## [1] FALSE

Logical operations on vectors

Logical operators are vectorised in R; when run on a vector, they return a logical vector of the same length …

a <= 2

##  first second  third 
##   TRUE   TRUE  FALSE

… which can be used to subset the original vector.

a[a <= 2]

##  first second 
##      1      2

Asking whether a variable is contained within a vector is an example of a set membership query and can be performed using the %in% operator. As with other logical operators, these are vectorised in R …

b = c(3, 4, 5)
a %in% b

## [1] FALSE FALSE  TRUE

… and can be used for subsetting.

a[a %in% b]

## third 
##     3

As stated, when run on a vector, these operations return a logical vector of the same length.

If it’s preferable to just have a list of the indices that satisfy a given logical criteria, the which() function can be used instead …

which(a %in% b)

## [1] 3

… which can be used to subset the original vector in exactly the same way.

a[which(a %in% b)]

## third 
##     3

Modifying logicals

Single logical variables or vectors of them can be combined and manipulated with the & (and), | (or), and ! (not) operators.

TRUE & FALSE  # do both objects evaluate to TRUE?

## [1] FALSE

c(TRUE, FALSE, FALSE) | c(TRUE, TRUE, FALSE)  # in pairs, does either evaluate to TRUE?

## [1]  TRUE  TRUE FALSE

!(1 > 2)  # the `not` operator inverts the answer

## [1] TRUE

Practical

Many Emperor penguins don’t start breeding until they’re 6 years old.

Which of your penguins are too young to breed?

To bump up your numbers, you decide to get more penguins.

Update your vector to add Erica (99) and Jen (107)

Reading data into vectors

Vectors can be created from simple text files by using the scan(file, what) function. We pass two important arguments:

file … the location of the file to be read
what … the basic data type that it contains: character, numeric, or logical

my_first_data = scan("data/1_scan.txt", "character")
my_first_data

## [1] "Wow"  "that" "was"  "very" "easy"

Data frames

The data.frame() function can be used to combine individual vectors into columns of a unified table.

Separate columns can be used to store different data types but each column is still an individual vector … and vectors can only store a single data type.

df = data.frame(col1=c(1, 2, 3), col2=c("one", "two", "three"))
df

##   col1  col2
## 1    1   one
## 2    2   two
## 3    3 three

class(df)

## [1] "data.frame"

As data frames are two dimensional, different functions are required to manipulate them.

Columns can be added using cbind() (column bind) …

df = cbind(df, col3=c(TRUE, FALSE, TRUE))
df

##   col1  col2  col3
## 1    1   one  TRUE
## 2    2   two FALSE
## 3    3 three  TRUE

… or using the special $ operator.

df$col4 = c(1.1, 1.2, 1.3)
df

##   col1  col2  col3 col4
## 1    1   one  TRUE  1.1
## 2    2   two FALSE  1.2
## 3    3 three  TRUE  1.3

Similarly, instead of names(), there are rownames() …

rownames(df) = c("a", "b", "c")
df

##   col1  col2  col3 col4
## a    1   one  TRUE  1.1
## b    2   two FALSE  1.2
## c    3 three  TRUE  1.3

… and colnames().

colnames(df) = toupper(colnames(df))
df

##   COL1  COL2  COL3 COL4
## a    1   one  TRUE  1.1
## b    2   two FALSE  1.2
## c    3 three  TRUE  1.3

In a data frame, column and row names must be unique. Duplicate names are not allowed!

Instead of length(), to get the size of a data frame, we can use nrow() …

nrow(df)

## [1] 3

… ncol() …

ncol(df)

## [1] 4

… or, to get both together, dim().

dim(df)

## [1] 3 4

Indexing data frames

To access the information within a data frame, as with vectors, we use square brackets ([ ]). However, we must now define both row and column positions:

[r, ] … index values before the comma refer to rows
[, c] … index values after the comma refer to columns
Omitting either one, as above, will return all possibilities.

df[2, ]  # take row 2, take all columns

##   COL1 COL2  COL3 COL4
## b    2  two FALSE  1.2

df[, 2]  # take all rows, take column 2

## [1] "one"   "two"   "three"

As with named vectors, we can also index by row and column name …

df[c("a", "b"), ]  # take the rows named "a" and "b"

##   COL1 COL2  COL3 COL4
## a    1  one  TRUE  1.1
## b    2  two FALSE  1.2

df[, "COL1"]  # take the column named "COL1"

## [1] 1 2 3

… and we can access columns individually with the $ operator, which returns the underlying vector.

df$COL1

## [1] 1 2 3

Reading data into data frames

Tabular plain-text formats can be exported from most software. In Excel it’s easy to export data as either tab-separated (.tsv / .txt) or as comma-separated (.csv) files directly when saving a document.

Tab-separated and comma-separated data can be imported using the read.delim() and read.csv() functions, respectively.

df = read.delim("data/1_read_delim.txt")

Data frames can be very large and cumbersome to view. To make things easier, we can use:

head() to display the first few rows
tail() to display the last few rows
View(), which in RStudio will open a separate tab to display the contents
str() to view its structure and the basic types of its component vectors
table() and summmary() to view compact representations of specified columns

head(df)

##   ID    Name Sex Age HatColour
## 1 E1   Basil   M  15      blue
## 2 E2     Tim   M  53       red
## 3 E3    Lisa   F  97    yellow
## 4 E4 Snapper   M  64     green
## 5 E5   Erica   F  99    yellow
## 6 E6     Jen   F 107       red

str(df)

## 'data.frame':    10 obs. of  5 variables:
##  $ ID       : chr  "E1" "E2" "E3" "E4" ...
##  $ Name     : chr  "Basil" "Tim" "Lisa" "Snapper" ...
##  $ Sex      : chr  "M" "M" "F" "M" ...
##  $ Age      : int  15 53 97 64 99 107 60 150 131 78
##  $ HatColour: chr  "blue" "red" "yellow" "green" ...

Merging data frames

Often, we need to merge data frames that have been stored separately. The merge() function will automate merger by matching up values from two tables based on a specified (key) column.

df2 = read.delim("data/1_read_delim_merge.txt")
colnames(df2)

## [1] "ID"     "Height" "Weight"

penguins = merge(df, df2, by="ID")
head(penguins)

##   ID    Name Sex Age HatColour Height Weight
## 1 E1   Basil   M  15      blue    120   35.6
## 2 E2     Tim   M  53       red    115   33.2
## 3 E3    Lisa   F  97    yellow    125   37.3
## 4 E4 Snapper   M  64     green    127   38.0
## 5 E5   Erica   F  99    yellow    110   30.1
## 6 E6     Jen   F 107       red    119   36.5

Practical

So, you’ve started to record things about your penguins. We’re not judging.

How many penguins do you now have?
Are you sure? What happens if you merge the data frames with merge(..., all=TRUE)?
Why is this different?
What are the average ages of the female and, separately, of the male penguins?
What function might we use to work out a unique list of the different hat colours they have?
How could we change the order of the rows if we wanted to arrange by age?
What does table(penguins$HatColour) do? How about table(penguins$Sex, penguins$HatColour)?

NA values

Data frames and vectors containing NA values can require special treatment when running functions or calculations.

penguins = merge(df, df2, by="ID", all=TRUE)
range(penguins$Height)

## [1] NA NA

mean(penguins$Height)

## [1] NA

We can sanitise an entire data frame by using the na.omit() function to drop all NA-containing rows …

penguins = na.omit(penguins)

… but, unless we want to discard data, it’s often better to just drop NAs for specific calculations. Many functions take the na.rm=TRUE argument to facilitate this

range(penguins$Height, na.rm=TRUE)

## [1] 110 130

Factors

Where vectors store categorical data, we can convert them to a special factor class, which allows their use with specialised functions.

A factor is suitable where we might logically group the rows by it:

Sex can be grouped … it’s a factor
Age is a continuous spread … it’s not a factor
ID is a unique identifier for each row, there’s probably no advantage to it being a factor

Further, there are two subclasses of factors:

nominal factors are inherently unordered (e.g. Sex)
ordinal factors are inherently ordered (e.g. timepoint)

Factors can be created using the factor() function on a vector …

penguins$Sex = factor(penguins$Sex)
penguins$Sex

##  [1] M F M F M F F M M F
## Levels: F M

class(penguins$Sex)

## [1] "factor"

… and its levels can be viewed.

levels(penguins$Sex)

## [1] "F" "M"

Ordering factors

The ordering of factor levels is important, as the first is taken as the reference. By default, levels are sorted numerically or lexicographically.

For nominal factors, this can be controlled by specifying either a different reference level …

relevel(penguins$Sex, "M")

##  [1] M F M F M F F M M F
## Levels: M F

… or by re-applying the factor() function and providing a different order.

factor(penguins$Sex, levels=c("M", "F"))

##  [1] M F M F M F F M M F
## Levels: M F

For ordinal factors, this is controlled by re-applying the function with factor(..., ordered=TRUE).

timepoint = factor(c("d0", "d1", "d3", "d7", "d10"))
timepoint

## [1] d0  d1  d3  d7  d10
## Levels: d0 d1 d10 d3 d7

timepoint = factor(
  timepoint,
  levels=c("d0", "d1", "d3", "d7", "d10"),
  ordered=TRUE)
timepoint

## [1] d0  d1  d3  d7  d10
## Levels: d0 < d1 < d3 < d7 < d10

is.ordered(timepoint)

## [1] TRUE

Modifying factors

The level of an element can be switched (provided the replacement level is already defined) in the same way a vector is modified.

timepoint[1] = "d3"
timepoint

## [1] d3  d1  d3  d7  d10
## Levels: d0 < d1 < d3 < d7 < d10

The levels() function can also be used to rename levels en masse and adjust the elements correspondingly.

levels(timepoint) = c("day0", "day1", "day3", "day7", "day10")
timepoint

## [1] day3  day1  day3  day7  day10
## Levels: day0 < day1 < day3 < day7 < day10

However, to change an individual element to a previously undefined level, it must be added first.

levels(timepoint) = c("day0", "day1", "day3", "day7", "day10", "day14")
timepoint[1] = "day14"
timepoint

## [1] day14 day1  day3  day7  day10
## Levels: day0 < day1 < day3 < day7 < day10 < day14

If, as a result of modification or subsetting, levels become unused, they can be removed using the droplevels() function.

timepoint = droplevels(timepoint)
timepoint

## [1] day14 day1  day3  day7  day10
## Levels: day1 < day3 < day7 < day10 < day14

Practical

You have realised that HatColour contains categorical data and should be turned into a vector.

Update the penguins data frame to make this change.
Is HatColour nominal or ordinal?
Penguin E1 (Basil) does not like having a blue hat and would prefer red. What steps do we need to take to fully update our data frame?

Plotting in base R

We will cover plotting in more detail using the ggplot2 library in Session 4. ‘Base’ R can still do some basic plotting, though, and has several types of graph built in:

plot() produces scatter plots
boxplot()
barplot()
histogram()

As with other functions, we can find out how to use these functions with the ? operator.

?boxplot

boxplot expects a formula (of the form y ~ x) as its single positional argument and we can pass a data frame to it using the data optional argument.

boxplot(Height~Sex, data=penguins)

plot, somewhat cryptically, says “any reasonable way of defining the coordinates is acceptable” when describing its input format. Sufficed to say that one reasonable way is to use a formula and data, as we did for the boxplot.

plot(Height~Weight, data=na.omit(penguins))

Columns defined as factors can be used to modify the aesthetics of the plot. For example, we can edit the colour and shape of points based on Sex. It makes sense to then also use the legend() function to show what we’ve done.

plot(Height~Weight, data=na.omit(penguins), col=c("purple", "green4")[Sex], pch=c("♀", "♂")[Sex])
legend("topleft", legend=levels(penguins$Sex), col=c("purple", "green4"), pch=c("♀", "♂"))

Homework

There are some penguin-related homework tasks to help cement what we’ve covered today!

The homework and instructions can be found within the main directory for the course: ./homework/Homework_1.Rmd

Introduction To R | Session 1

LMS Bioinformatics Facility

2023-10-23

First things first

Learning objectives

RStudio

Assignment

Comments

Object naming

Functions

Practical

Basic data types

Vectors

Practical

R is vectorised

Indexing vectors

Practical

Index-based replacement

Logical operations

Logical operations on vectors

Modifying logicals

Practical

Reading data into vectors

Data frames

Indexing data frames

Reading data into data frames

Merging data frames

Practical

NA values

Factors

Ordering factors

Modifying factors

Practical

Plotting in base R

Homework